jbrowse-plugin-graphgenomeviewer 4.0.6 → 4.0.8

package/README.md

@@ -1,267 +1,69 @@
 # jbrowse-plugin-graphgenomeviewer
 
-A JBrowse 2 plugin that draws a pangenome graph (GFA / rGFA) as a track of a
-linear genome view, and as a **GraphGenomeView** of its own for a whole file.
-
-## Screenshots
-
-The LPA KIV-2 window of the HPRC release 2 graph in the **force-directed
-layout**: the GRCh38 backbone runs left to right, coloured by position the way
-the rGFA segments track above it is, and the kringle repeat array is the knot of
-loops in the middle. Each bubble the graph holds is haloed along its own nodes
-and labelled by what it is; the label opens the bubble on its own.
+Pangenome graphs in JBrowse 2.
 
 ![KIV-2, force-directed, with its bubbles marked](img/force_kiv2.png)
 
-Clicking the array's label opens its 29 segments in the same layout, with a
-button back to the window. A popped graph derives its own bubbles, so a
-superbubble opens level by level:
-
-![The KIV-2 array popped open](img/force_kiv2_popped.png)
-
-Over a gbz-base database the cut carries the haplotypes' walks. A node draws
-thicker the more of them carry it, Bandage's depth as width, and every route
-through a bubble is labelled at the far point of its loop for the haplotypes
-that take it and how long it is, so the array reads as one copy count per
-haplotype:
-
-![KIV-2 over gbz-base, eight haplotypes, force-directed](img/force_kiv2_gbz.png)
-
-Picking one walk lifts it out of the drawing. HG00133's route through the window
-keeps its ink and the other haplotypes fade; the readout says it carries 116 kb
-more than GRCh38 through the array:
-
-![HG00133's walk lifted out of the KIV-2 cut](img/force_kiv2_walk.png)
-
-MHC class II, where one 254-segment superbubble covers the DRB haplotype block
-and a run of small indels follows it. The session's gene track is drawn onto the
-graph: exons as dark stretches along the backbone nodes that carry them, and
-each gene's name pinned under the backbone at its midpoint, so the superbubble
-reads as HLA-DRB5's and the indels as HLA-DRB6's and HLA-DRB1's:
+![Tube maps, and a tube map track under a linear view](img/tube_map.png)
 
-![MHC class II, force-directed, with genes on the backbone](img/force_mhc.png)
+- Eight layouts: force-directed (Bandage FMMM), variant map, ordered, anchored,
+  sample rows, walk rows, and sequenceTubeMap's tube map on its own axis or the
+  reference's
+- Bubbles from `gfatools bubble` or the graph itself, opened level by level
+- gbz-base haplotypes as walks: carriage as node thickness, one walk lifted out
 
-The KIV-2 window as a **variant map**, the reference as one line with one typed
-glyph per bubble:
+## Usage
 
-![Variant map of KIV-2](img/variant_map_kiv2.png)
-
-It ships six layouts:
-
-- **Force-directed**: the graph's shape, computed by the OGDF FMMM engine from
-  [Bandage](https://github.com/rrwick/Bandage), seeded along the reference and
-  turned to read left to right. The engine lays out unbranching runs rather than
-  nodes, so a base-level cut of 15,000 nodes draws in a few seconds. The Walk
-  picker lifts one haplotype out: its route keeps its ink, the rest fades, and a
-  readout gives its length against the reference.
-- **Variant map** (rGFA or a reference path): the reference as a line, one typed
-  glyph per bubble, click to open a bubble's graph, and again for a bubble
-  inside it.
-- **Ordered** (rGFA or a reference path): x is reference order rather than bp,
-  so every node gets room and a bubble reads as a lens. Scrolls sideways.
-- **Anchored** (rGFA or a reference path): x is reference bp, one row per stable
-  rank, aligned under a linear view.
-- **Sample rows**: x is reference bp, one row per contributing assembly.
-- **Walk rows** (W or P lines): x is each walk's own bp, one bar per haplotype,
-  sequence the reference also carries in blue and sequence it does not in
-  purple, so a repeat expansion reads as bar length. The Repeat picker tiles the
-  bars by a repeat annotation's unit and marks the allele a genotyper called.
-
-The bubbles come from `gfatools bubble` output beside the rGFA index
-(`<prefix>.bubbles.bed.gz`), which HPRC's hosted graph has and
-`scripts/build_rgfa_tabix.sh` in jbrowse-components writes, or, for a graph with
-no index, a GBZ cut, a pggb file or a popped bubble, from the graph itself off
-the ordered layout's layering. Every node layout marks them as halos; the
-variant map draws them as glyphs.
-
-### The graph as a track
-
-A graph track's display is `LinearGraphDisplay`. It cuts the view's window plus
-a window-width each side and re-cuts once the view leaves the cut, keeping its
-sample rows in the order they were drawn. On a layout whose x is reference bp,
-such as Anchored, Sample rows, Walk rows or the Variant map, the graph draws
-under the view's own coordinates and pans and zooms with it. The force-directed
-and ordered layouts draw in their own coordinates inside the track, fitted to
-it, with their own zoom in the track menu, the way a variant matrix does. The
-track menu also picks the layout, the colour, a walk to lift out, and opens the
-settings.
+Needs JBrowse 5.0.0-beta.9 or later.
 
 ```json
 {
-  "type": "FeatureTrack",
-  "trackId": "hprc_graph",
-  "name": "HPRC release 2 graph",
-  "assemblyNames": ["hg38"],
-  "adapter": { "type": "RgfaTabixAdapter", "uri": "https://example.com/hprc" },
-  "displays": [
-    {
-      "type": "LinearGraphDisplay",
-      "displayId": "hprc_graph-LinearGraphDisplay"
-    },
+  "plugins": [
     {
-      "type": "LinearBasicDisplay",
-      "displayId": "hprc_graph-LinearBasicDisplay"
+      "name": "GraphGenomeView",
+      "esmUrl": "https://unpkg.com/jbrowse-plugin-graphgenomeviewer/dist/jbrowse-plugin-graphgenomeviewer.esm.js"
     }
   ]
 }
 ```
 
-The first display is the one the track opens with; the second is the segments
-lane, one block per segment, reachable from the track menu.
-
-A fine cut spans at most 5 Mb. An rGFA track can carry a coarse tier, one node
-per bubble, built by `build_bubble_tier.sh` in jbrowse-components; past
-`aboveBpPerPx` in the linear view the track cuts that pair instead, with no bp
-cap:
-
-```json
-{
-  "type": "RgfaTabixAdapter",
-  "uri": "https://example.com/hprc-v2.0-mc-grch38",
-  "coarse": {
-    "uri": "https://example.com/hprc-v2.0-mc-grch38.tier10000",
-    "aboveBpPerPx": 1000
-  }
-}
-```
-
-**Add → Graph genome view** opens a whole GFA file in a view of its own, with
-the same layouts and its own pan and zoom.
-
-### Demonstration loci
-
-Six HPRC release 2 windows, the ones the
-[HPRC tutorials](https://jbrowse.org/jb2/docs/tutorials/pangenome_hprc/) walk
-through, are the standing test set for layout screenshots. Each cuts to under
-300 nodes and shows a different kind of variation:
-
-| Locus        | Window                         | What it shows                       |
-| ------------ | ------------------------------ | ----------------------------------- |
-| LPA KIV-2    | `chr6:160,525,000-160,655,000` | the kringle repeat, copy per loop   |
-| MHC class II | `chr6:32,510,000-32,600,000`   | DRB haplotypes, dozens of alleles   |
-| AMY1         | `chr1:103,690,000-103,780,000` | amylase copy number                 |
-| C4           | `chr6:31,980,000-32,050,000`   | one bubble over the C4 duplication  |
-| CFH          | `chr1:196,640,000-196,900,000` | an 84 kb deletion as a bare edge    |
-| KIR          | `chr19:54,750,000-54,840,000`  | the KIR cluster, densest of the six |
-
-[docs/layout-experiments.md](docs/layout-experiments.md) draws all six in every
-layout the plugin has and in the ones proposed to replace them, and
-`scripts/layout-lab/` reproduces the figures.
-
-## License (GPL-3.0)
-
-This plugin is **GPL-3.0-or-later**. The force-directed layout is computed by a
-WebAssembly build of Bandage's FMMM layout from [OGDF](https://ogdf.github.io/),
-and both Bandage and OGDF are GPL-licensed, so this plugin takes the same
-license rather than linking around it.
-
-JBrowse itself is unaffected and stays Apache-2.0: this is a separate plugin,
-loaded at runtime only by configs that ask for it. The anchored and sample-row
-layouts are pure TypeScript and need no external engine.
-
-## Developing
-
-Requires [pnpm](https://pnpm.io/installation). The plugin builds against the
-published `@jbrowse/*` packages at 5.0.0-beta.9 and needs a host of at least
-that version: it hands its RPC calls an AbortSignal, which an earlier JBrowse 5
-beta cannot post to its worker.
-
-```console
-pnpm install
-pnpm start        # esbuild watch, serves dist/out.js on :9000 with CORS
-```
-
-In another terminal, serve a JBrowse Web that points at `config.json` (its
-`plugins` entry already targets `http://localhost:9000/dist/out.js`).
-
-## Building
-
-```console
-pnpm build        # native ESM bundle via esbuild (code-split)
-pnpm typecheck    # tsc, separately — esbuild strips types without checking them
-```
-
-This writes the plugin to `dist/`, and the **whole directory must be served
-together** — the entry loads its sibling chunks relative to its own url:
-
-- `jbrowse-plugin-graphgenomeviewer.esm.js` — the plugin entry
-- `chunks/bandage-layout-<hash>.js` — the Bandage layout engine (~425kb),
-  imported on demand and named by content hash so a redeployed engine is never
-  served from cache
-- `chunks/*.js` — other lazily-loaded code split out of the entry
-
-Load the plugin from any JBrowse config, 5.0.0-beta.9 or later, with an
-`esmUrl`:
+- **File → Open track** opens an rGFA index (`.segs.bed.gz` from
+  `build_rgfa_tabix.sh`) or a gbz-base database (`.gbz.db`) as a `GraphTrack`
+- **Add → Graph genome view** opens a whole GFA file
+- A hand-written track needs only the adapter:
 
 ```json
 {
-  "plugins": [
-    {
-      "name": "GraphGenomeView",
-      "esmUrl": "https://unpkg.com/jbrowse-plugin-graphgenomeviewer/dist/jbrowse-plugin-graphgenomeviewer.esm.js"
+  "type": "GraphTrack",
+  "trackId": "hprc_graph",
+  "name": "HPRC release 2 graph",
+  "assemblyNames": ["hg38"],
+  "adapter": {
+    "type": "RgfaTabixAdapter",
+    "uri": "https://example.com/hprc",
+    "coarse": {
+      "uri": "https://example.com/hprc.tier10000",
+      "aboveBpPerPx": 1000
     }
-  ]
+  }
 }
 ```
 
-Note: ESM plugins are loaded via a dynamic `import()`, which cannot carry a
-subresource-integrity hash the way a UMD `<script integrity>` can — there is
-nowhere to put a digest. For a deployment that needs pinned, tamper-evident
-bytes, serve the plugin from an immutable, version-pinned url on a host you
-control. The engine chunk is already immutable by content hash.
-
-The engine is a lazy chunk: it is only fetched the first time someone selects
-the force-directed layout, so sessions that use the anchored or sample-row
-layouts never download it. Its url is not configured anywhere — `loadBandage` is
-a plain dynamic `import()`, so the browser resolves the chunk relative to the
-plugin module's own url (`import.meta.url`, defined on the main thread and in
-the RPC worker alike). That is why the whole `dist/` has to be served together,
-and it is also why there is nothing to point elsewhere: to host the engine on
-another origin, rebuild with the chunk emitted there.
-
-### Rebuilding the engine
-
-`src/bandage/bandage-layout.js` is a committed build artifact, so a normal
-`pnpm build` never needs Emscripten. Regenerate it only when the C++ layout
-sources change:
-
-```console
-pnpm build:wasm   # needs emsdk, nothing else
-```
-
-Emscripten is the only thing you have to install. OGDF is vendored at
-`vendor/ogdf` (a stock checkout of it does not build for wasm at all — see
-[`vendor/README.md`](vendor/README.md)), so this works offline from a fresh
-clone of this repo alone. Roughly four minutes the first time, seconds after
-that.
-
-It compiles with `-sSINGLE_FILE=1`, embedding the wasm as base64 so the result
-is one self-contained ES module that esbuild can copy rather than bundle.
+- The track menu picks layout, colour and walk, and switches to the segments
+  lane or, for gbz-base, the haplotype lanes
+- Cuts the window plus a window each side, up to 5 Mb; past `aboveBpPerPx`, the
+  `coarse` tier (`build_bubble_tier.sh` in jbrowse-components)
+- gbz-base swaps in `{ "type": "GbzBaseSyntenyAdapter", "uri": "….gbz.db" }`; an
+  `hg38` or `hs1` track finds the graph's GRCh38 or CHM13 reference sample, and
+  `assemblyNameToPanSN` covers other names
 
-A rebuild has to be checked against the drawing rather than against the file,
-since the artifact's bytes move for reasons the layout does not — see
-[`src/bandage/README.md`](src/bandage/README.md) for
-`scripts/layout-digest.mjs`.
+## Docs
 
-## Testing
-
-```console
-pnpm test         # vitest unit tests
-pnpm test:watch
-pnpm test:wasm    # runs the committed Bandage engine, no deps needed
-pnpm test:e2e     # puppeteer, opt-in — see test/README.md
-pnpm host-compat  # boots dist/ on the hosted JBrowse releases and cuts a graph
-pnpm lint
-pnpm typecheck
-```
+- [docs/layouts.md](docs/layouts.md) — layouts, bubbles, walks, genes, loci
+- [docs/developing.md](docs/developing.md) — building, testing, `host-compat`
+- [docs/layout-experiments.md](docs/layout-experiments.md) — every locus in
+  every layout
 
-`pnpm test:e2e` drives the force layout through a real JBrowse in a headless
-browser, behind `RUN_E2E=1` because it needs a jbrowse-web build to serve;
-[`test/README.md`](test/README.md) explains how to run it.
+## License
 
-`pnpm host-compat` is the check a publish has to pass, and `pnpm version` runs
-it. It serves the built `dist/` to a real shipped config on each hosted release
-and cuts a subgraph there, because the failures it catches pass tsc, eslint and
-the unit tests: an RPC argument a released core cannot post to its worker, or a
-re-export the host no longer serves, shows only when the bundle runs on the
-host.
+GPL-3.0-or-later (the wasm FMMM engine is OGDF, GPL).

package/dist/chunks/AddTrackWorkflow-LRRSAVSX.js

@@ -0,0 +1,2 @@
+import{a as F,b as T,e as y}from"./chunk-JVMMNMQG.js";import"./chunk-D7XFR2IV.js";import{a as N}from"./chunk-J4OLMLS5.js";import{a as W}from"./chunk-FCWXYIFC.js";import{a as C,b as B,c as H,d as _,e as O}from"./chunk-XEJ47DLD.js";import{a as w,b as t}from"./chunk-FY3BTKY4.js";var S=w((q,L)=>{L.exports=JBrowseExports["@jbrowse/core/util/tss-react"]});var s=t(O(),1),i=t(_(),1),l=t(N(),1),A=t(S(),1),R=t(W(),1),e=t(H(),1),x=t(B(),1);var o=t(C(),1),j=(0,A.makeStyles)()(n=>({paper:{margin:n.spacing(),padding:n.spacing()},field:{marginTop:n.spacing(2)},submit:{marginTop:25,marginBottom:100,display:"block"}})),D=["RgfaTabixAdapter","MinigraphBubbleAdapter"],J=(0,x.observer)(function({model:r}){let{classes:c}=j(),h=(0,l.getSession)(r),b=(0,R.getRoot)(r),[m,G]=(0,s.useState)("RgfaTabixAdapter"),[p,v]=(0,s.useState)(),[g,P]=(0,s.useState)(),[u,I]=(0,s.useState)(""),[d,M]=(0,s.useState)("Pangenome graph"),[f,k]=(0,s.useState)();function E(){if(!(!p||!r.assembly))try{k(void 0);let a=d.trim();(0,l.addTrackFromWidget)({model:r,session:h,conf:y({choice:m,loc:p,indexLoc:g,assembly:r.assembly,sample:u,trackId:(0,l.makeTrackId)({name:a}),name:a})})}catch(a){k(a)}}return(0,o.jsxs)(e.Paper,{className:c.paper,children:[f?(0,o.jsx)(i.ErrorMessage,{error:f}):null,(0,o.jsxs)(e.FormControl,{children:[(0,o.jsx)(e.FormLabel,{children:"File type"}),(0,o.jsx)(e.RadioGroup,{value:m,onChange:a=>{G(a.target.value)},children:D.map(a=>(0,o.jsx)(e.FormControlLabel,{value:a,control:(0,o.jsx)(e.Radio,{}),label:F[a]},a))})]}),(0,o.jsx)(i.FileSelector,{location:p,name:T[m],rootModel:b,setLocation:v}),(0,o.jsx)(i.FileSelector,{location:g,name:"Path to tabix index (optional; the sibling .tbi is assumed, a .csi is recognised by name)",rootModel:b,setLocation:P}),(0,o.jsx)(e.TextField,{className:c.field,value:u,onChange:a=>{I(a.target.value)},label:"Sample name in the graph",slotProps:{htmlInput:{"data-testid":"graph-sample-input"}},helperText:"Optional. The PanSN prefix the graph gives this assembly, e.g. GRCh38 for HPRC's GRCh38#0#chr1; leave blank when the graph's stable names are bare",placeholder:"GRCh38",fullWidth:!0}),(0,o.jsx)(e.TextField,{className:c.field,value:d,helperText:"Track name",slotProps:{htmlInput:{"data-testid":"graph-track-name-input"}},onChange:a=>{M(a.target.value)}}),(0,o.jsx)(i.AssemblySelector,{session:h,helperText:"Select assembly to add track to",selected:r.assembly,onChange:a=>{r.setAssembly(a)},fullWidth:!0}),(0,o.jsx)(e.Button,{variant:"contained",className:c.submit,disabled:!p||!d.trim()||!r.assembly,onClick:E,children:"Submit"})]})}),K=J;export{K as default};
+//# sourceMappingURL=AddTrackWorkflow-LRRSAVSX.js.map

package/dist/chunks/AddTrackWorkflow-LRRSAVSX.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["global-externals:@jbrowse/core/util/tss-react", "../../src/GraphAddTrackWorkflow/AddTrackWorkflow.tsx"],
+  "sourcesContent": ["module.exports = JBrowseExports[\"@jbrowse/core/util/tss-react\"];", "import { useState } from 'react'\n\nimport { AssemblySelector, ErrorMessage, FileSelector } from '@jbrowse/core/ui'\nimport { addTrackFromWidget, getSession, makeTrackId } from '@jbrowse/core/util'\nimport { makeStyles } from '@jbrowse/core/util/tss-react'\nimport { getRoot } from '@jbrowse/mobx-state-tree'\nimport {\n  Button,\n  FormControl,\n  FormControlLabel,\n  FormLabel,\n  Paper,\n  Radio,\n  RadioGroup,\n  TextField,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport {\n  GRAPH_FILE_FIELDS,\n  GRAPH_FILE_LABELS,\n  buildTrackConfig,\n} from './buildTrackConfig'\n\nimport type { GraphFileChoice } from './buildTrackConfig'\nimport type {\n  AbstractRootModel,\n  AddTrackWorkflowModel,\n  FileLocation,\n} from '@jbrowse/core/util'\n\nconst useStyles = makeStyles()(theme => ({\n  paper: {\n    margin: theme.spacing(),\n    padding: theme.spacing(),\n  },\n  field: {\n    marginTop: theme.spacing(2),\n  },\n  submit: {\n    marginTop: 25,\n    marginBottom: 100,\n    display: 'block',\n  },\n}))\n\nconst CHOICES: GraphFileChoice[] = [\n  'RgfaTabixAdapter',\n  'MinigraphBubbleAdapter',\n]\n\nconst GraphAddTrackWidget = observer(function GraphAddTrackWidget({\n  model,\n}: {\n  model: AddTrackWorkflowModel\n}) {\n  const { classes } = useStyles()\n  const session = getSession(model)\n  const rootModel = getRoot<AbstractRootModel>(model)\n  const [choice, setChoice] = useState<GraphFileChoice>('RgfaTabixAdapter')\n  const [loc, setLoc] = useState<FileLocation>()\n  const [indexLoc, setIndexLoc] = useState<FileLocation>()\n  const [sample, setSample] = useState('')\n  const [trackName, setTrackName] = useState('Pangenome graph')\n  const [error, setError] = useState<unknown>()\n\n  function handleSubmit() {\n    if (!loc || !model.assembly) {\n      return\n    }\n    try {\n      setError(undefined)\n      const name = trackName.trim()\n      addTrackFromWidget({\n        model,\n        session,\n        conf: buildTrackConfig({\n          choice,\n          loc,\n          indexLoc,\n          assembly: model.assembly,\n          sample,\n          trackId: makeTrackId({ name }),\n          name,\n        }),\n      })\n    } catch (e) {\n      setError(e)\n    }\n  }\n\n  return (\n    <Paper className={classes.paper}>\n      {error ? <ErrorMessage error={error} /> : null}\n      <FormControl>\n        <FormLabel>File type</FormLabel>\n        <RadioGroup\n          value={choice}\n          onChange={event => {\n            setChoice(event.target.value as GraphFileChoice)\n          }}\n        >\n          {CHOICES.map(option => (\n            <FormControlLabel\n              key={option}\n              value={option}\n              control={<Radio />}\n              label={GRAPH_FILE_LABELS[option]}\n            />\n          ))}\n        </RadioGroup>\n      </FormControl>\n      <FileSelector\n        location={loc}\n        name={GRAPH_FILE_FIELDS[choice]}\n        rootModel={rootModel}\n        setLocation={setLoc}\n      />\n      <FileSelector\n        location={indexLoc}\n        name=\"Path to tabix index (optional; the sibling .tbi is assumed, a .csi is recognised by name)\"\n        rootModel={rootModel}\n        setLocation={setIndexLoc}\n      />\n      <TextField\n        className={classes.field}\n        value={sample}\n        onChange={event => {\n          setSample(event.target.value)\n        }}\n        label=\"Sample name in the graph\"\n        slotProps={{ htmlInput: { 'data-testid': 'graph-sample-input' } }}\n        helperText=\"Optional. The PanSN prefix the graph gives this assembly, e.g. GRCh38 for HPRC's GRCh38#0#chr1; leave blank when the graph's stable names are bare\"\n        placeholder=\"GRCh38\"\n        fullWidth\n      />\n      <TextField\n        className={classes.field}\n        value={trackName}\n        helperText=\"Track name\"\n        slotProps={{ htmlInput: { 'data-testid': 'graph-track-name-input' } }}\n        onChange={event => {\n          setTrackName(event.target.value)\n        }}\n      />\n      <AssemblySelector\n        session={session}\n        helperText=\"Select assembly to add track to\"\n        selected={model.assembly}\n        onChange={arg => {\n          model.setAssembly(arg)\n        }}\n        fullWidth\n      />\n      <Button\n        variant=\"contained\"\n        className={classes.submit}\n        disabled={!loc || !trackName.trim() || !model.assembly}\n        onClick={handleSubmit}\n      >\n        Submit\n      </Button>\n    </Paper>\n  )\n})\n\nexport default GraphAddTrackWidget\n"],
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+  "names": ["require_tss_react", "__commonJSMin", "exports", "module", "import_react", "import_ui", "import_util", "import_tss_react", "import_mobx_state_tree", "import_material", "import_mobx_react", "import_jsx_runtime", "useStyles", "theme", "CHOICES", "GraphAddTrackWidget", "model", "classes", "session", "rootModel", "choice", "setChoice", "loc", "setLoc", "indexLoc", "setIndexLoc", "sample", "setSample", "trackName", "setTrackName", "error", "setError", "handleSubmit", "name", "buildTrackConfig", "e", "event", "option", "GRAPH_FILE_LABELS", "GRAPH_FILE_FIELDS", "arg", "AddTrackWorkflow_default"]
+}